{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,26]],"date-time":"2026-10-26T01:46:53Z","timestamp":1792979213660,"version":"4.5.0"},"posted":{"date-parts":[[2022,1,1]]},"reference-count":0,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2022,1,1]],"date-time":"2022-01-01T00:00:00Z","timestamp":1640995200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"\n Homepage<\/ns3:bold>\n :\n https:\/\/edamontology.org\/<\/ns3:ext-link>\n <\/ns3:p>\n \n Source Code<\/ns3:bold>\n :\n https:\/\/github.com\/edamontology\/edamontology<\/ns3:ext-link>\n <\/ns3:p>\n \n License<\/ns3:bold>\n :\n CC BY-SA 4.0<\/ns3:ext-link>\n <\/ns3:p>\n \n \n EDAM [\n 1<\/ns3:ext-link>\n ] is a domain ontology of data analysis and data management in bio- and other sciences, and science-based applications. It comprises concepts related to analysis, modelling, optimisation, and data life-cycle. Targetting usability by diverse end users, the structure of EDAM is relatively simple, divided into 4 main sections:\n \n \n \n \n Topic<\/ns3:italic>\n <\/ns3:bold>\n <\/ns3:p>\n <\/ns3:list-item>\n \n \n \n Operation<\/ns3:italic>\n <\/ns3:bold>\n <\/ns3:p>\n <\/ns3:list-item>\n \n \n \n Data<\/ns3:italic>\n <\/ns3:bold>\n (incl.\n Identifier<\/ns3:italic>\n )\n <\/ns3:p>\n <\/ns3:list-item>\n \n \n \n Format<\/ns3:bold>\n <\/ns3:italic>\n <\/ns3:p>\n <\/ns3:list-item>\n <\/ns3:list>\n <\/ns3:p>\n \n EDAM is used in numerous resources, for example\n Bio.tools<\/ns3:ext-link>\n ,\n Galaxy<\/ns3:ext-link>\n ,\n Debian<\/ns3:ext-link>\n , or the ELIXIR Europe training portal\n TeSS<\/ns3:ext-link>\n . Thanks to the annotations with EDAM,\n computational tools<\/ns3:bold>\n ,\n workflows<\/ns3:bold>\n ,\n standards<\/ns3:bold>\n ,\n data<\/ns3:bold>\n , and\n learning materials<\/ns3:bold>\n are easier to find, compare, choose, and integrate. EDAM contributes to\n open science<\/ns3:bold>\n by allowing semantic annotation of processed data, thus making the data more understandable, findable, and comparable. EDAM and its applications\n lower the barrier<\/ns3:bold>\n and effort for scientists and citizens alike, towards doing scientific research in a more\n open<\/ns3:italic>\n ,\n reliable<\/ns3:italic>\n , and\n inclusive<\/ns3:italic>\n way.\n <\/ns3:p>\n \n \n The main improvements in 2021 include:\n \n \n \n The addition of essential concepts of\n data management<\/ns3:italic>\n and\n open science<\/ns3:italic>\n <\/ns3:p>\n <\/ns3:list-item>\n \n \n Improved automated\n validation<\/ns3:bold>\n (CI)\n <\/ns3:p>\n <\/ns3:list-item>\n \n \n Improved contribution processes towards more\n inclusion<\/ns3:bold>\n and\n engagement<\/ns3:bold>\n with communities of scientific experts, software engineers, and volunteers\n <\/ns3:p>\n <\/ns3:list-item>\n \n \n Easier to\n contribute<\/ns3:bold>\n , and therefore new contributors and\n <\/ns3:p>\n \n new\n collaborations<\/ns3:bold>\n . And welcoming more!\n <\/ns3:p>\n <\/ns3:list-item>\n \n News from the applications: Galaxy can now visualise the tools panel sorted by EDAM.<\/ns3:p>\n <\/ns3:list-item>\n <\/ns3:list>\n <\/ns3:p>\n \n The\n EDAM community<\/ns3:bold>\n brings together software engineers and science experts (academic, industrial, citizen), professionals and volunteers. It can be followed and contributed to via various channels. One option is\n \n GitHub<\/ns3:underline>\n <\/ns3:ext-link>\n , with dedicated repositories incl.\n \n edamontology<\/ns3:underline>\n <\/ns3:ext-link>\n and others. Other platforms for contributions to EDAM are especially the generic ontology browsers of the NCBO BioPortal (\n \n EDAM<\/ns3:underline>\n <\/ns3:ext-link>\n ,\n \n EDAM Bioimaging<\/ns3:underline>\n <\/ns3:ext-link>\n [\n 2<\/ns3:ext-link>\n ]) and WebProt\u00e9g\u00e9 (\n \n EDAM<\/ns3:underline>\n <\/ns3:ext-link>\n ,\n \n EDAM Bioimaging<\/ns3:underline>\n <\/ns3:ext-link>\n ; free registration required also for viewing). The main communication channel is\n Gitter<\/ns3:ext-link>\n .\n <\/ns3:p>\n \n Along with the ontology, the community has developed a number of tools that enhance user experience with EDAM:\n \n \n \n \n EDAM Browser<\/ns3:bold>\n <\/ns3:ext-link>\n [\n 3<\/ns3:ext-link>\n ] is a lightweight and fast web-based ontology browser that provides a number of user-oriented features such as aggregated search across various EDAM-annotated resources (\n e.g<\/ns3:italic>\n .\n Bio.tools<\/ns3:ext-link>\n ,\n TeSS<\/ns3:ext-link>\n ), and\n suggesting changes<\/ns3:bold>\n to EDAM.\n <\/ns3:p>\n <\/ns3:list-item>\n \n \n \n EDAMmap<\/ns3:bold>\n <\/ns3:ext-link>\n is a tool for text mining EDAM concepts from articles.\n <\/ns3:p>\n <\/ns3:list-item>\n \n \n EDAM Popovers<\/ns3:bold>\n is a web-browser\n add-on<\/ns3:ext-link>\n \/<\/ns3:bold>\n extension<\/ns3:ext-link>\n for showing details of EDAM concepts found in a website. Great\n e.g.<\/ns3:italic>\n for code and textual data on GitHub\n <\/ns3:p>\n <\/ns3:list-item>\n <\/ns3:list>\n \n References:<\/ns3:bold>\n <\/ns3:sub>\n <\/ns3:p>\n \n \n [\n 1<\/ns3:ext-link>\n ] Ison, J., Kala\u0161, M., Jonassen, I., Bolser, D., Uludag, M., McWilliam, H., Malone, J., Lopez, R., Pettifer, S. and Rice, P. (\n 2013<\/ns3:bold>\n ). EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats.\n Bioinformatics<\/ns3:italic>\n ,\n 29<\/ns3:bold>\n (10): 1325-1332. DOI:\n 10.1093\/bioinformatics\/btt113<\/ns3:ext-link>\n Open access<\/ns3:italic>\n <\/ns3:sub>\n <\/ns3:p>\n \n \n [\n 2<\/ns3:ext-link>\n ] Mat\u00fa\u0161 Kala\u0161, Laure Plantard, Joakim Lindblad, Martin Jones, Nata\u0161a Sladoje, Moritz A. Kirschmann, Anatole Chessel, Leandro Scholz, Fabienne R\u00f6ssler, Laura Nicol\u00e1s S\u00e1enz, Estibaliz G\u00f3mez de Mariscal, John Bogovic, Alexandre Dufour, Xavier Heiligenstein, Dominic Waithe, Marie-Charlotte Domart, Matthia Karreman, Raf Van de Plas, Robert Haase, David H\u00f6rl, Lassi Paavolainen, Ivana Vrhovac Maduni\u0107, Dean Karaica, Arrate Mu\u00f1oz-Barrutia, Paula Sampaio, Daniel Sage, Sebastian Munck, Ofra Golani, Josh Moore, Florian Levet, Jon Ison, Alban Gaignard, Herv\u00e9 M\u00e9nager, Chong Zhang, Kota Miura, Julien Colombelli, Perrine Paul-Gilloteaux, and welcoming new contributors! (\n 2020<\/ns3:bold>\n )\n .<\/ns3:italic>\n EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats (update 2020) [version 1; not peer reviewed].\n F1000Research<\/ns3:italic>\n ,\n 9<\/ns3:bold>\n (ELIXIR):162 (Poster) DOI:\n 10.7490\/f1000research.1117826.1<\/ns3:ext-link>\n Open access<\/ns3:italic>\n <\/ns3:sub>\n <\/ns3:p>\n \n \n [\n 3<\/ns3:ext-link>\n ] Brancotte, B., Blanchet, C. and M\u00e9nager, H. (\n 2018<\/ns3:bold>\n ). A reusable tree-based web-visualization to browse EDAM ontology, and contribute to it.\n J. Open Source Softw.<\/ns3:italic>\n ,\n 3<\/ns3:bold>\n (27): 698. DOI:\n 10.21105\/joss.00698<\/ns3:ext-link>\n Open access<\/ns3:italic>\n <\/ns3:sub>\n <\/ns3:p>\n \n \n <\/ns3:p>\n \n \n Acknowledgement:<\/ns3:bold>\n <\/ns3:sub>\n <\/ns3:p>\n \n EDAM maintainers and interns were supported by ELIXIR Europe, Norway, and France.<\/ns3:sub>\n <\/ns3:p>\n \n \n Dr. Melissa Black and Gloria Umutesi were awarded with complimentary registration at ISMB\/ECCB 2021, funded by the\n BOSC 2021 sponsors<\/ns3:ext-link>\n .\n <\/ns3:sub>\n <\/ns3:p>\n \n The list of co-authors includes the substantial contributors to EDAM in 2020-2021 (version 1.26), without the contributors specific to EDAM Biomaging, EDAM Browser, or EDAMmap.<\/ns3:sub>\n <\/ns3:p>","DOI":"10.7490\/f1000research.1118900.1","type":"posted-content","created":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T21:17:08Z","timestamp":1763759828000},"source":"Crossref","is-referenced-by-count":10,"title":["EDAM: the bioscientific data analysis ontology (update 2021)"],"prefix":"10.7490","author":[{"given":"Melissa","family":"Black","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucie","family":"Lamothe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hager","family":"Eldakroury","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mads","family":"Kierkegaard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ankita","family":"Priya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne","family":"Machinda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Uttam","family":"Singh Khanduja","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Drashti","family":"Patoliya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rashika","family":"Rathi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tawah Peggy","family":"Che Nico","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gloria","family":"Umutesi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudia","family":"Blankenburg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anita","family":"Op","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Precious","family":"Chieke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Omodolapo","family":"Babatunde","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steve","family":"Laurie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steffen","family":"Neumann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Veit","family":"Schw\u00e4mmle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivan","family":"Kuzmin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chris","family":"Hunter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan","family":"Karr","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jon","family":"Ison","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alban","family":"Gaignard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bryan","family":"Brancotte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Herv\u00e9","family":"M\u00e9nager","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mat\u00fa\u0161","family":"Kala\u0161","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","container-title":[],"original-title":[],"deposited":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T21:17:27Z","timestamp":1763759847000},"score":1,"resource":{"primary":{"URL":"https:\/\/f1000research.com\/posters\/11-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,1,1]]},"references-count":0,"URL":"https:\/\/doi.org\/10.7490\/f1000research.1118900.1","relation":{},"subject":[],"published":{"date-parts":[[2022,1,1]]},"subtype":"other"}}